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Collaborative Environment for Ecosystem
System Science Analysis and Synthesis
(CoESRA)
Presentation by Siddeswara Guru
Outline
• Motivation
• Reproducible science
• Challenges
• CoESRA
• Use Case: IUCN Red List of Ecosystems
Assessment.
• Su...
Motivation
Reproducible Science
Duplicate the scientific experiments or
reproduce experiment results.
Source: nature.com
Challenges
• Lack of culture to make scientific
claims reproducible
• Lack of detailed information about
data and code eve...
Reproducibility Spectrum
Peng, Roger D. (2011). Reproducible Research in Computational Science.
Science, 334(6060), 1226-1...
Integrated Infrastructure
• Cloud-based platform
• Scientific workflows executable
on a easily accessible platform
"one of...
Scientific workflow
• Series of structured
interconnected
computational activities
• Visual front-end to build
experiments...
Kepler Scientific workflow
Features
• Ability to create
components in different
programming languages
• Reusable component...
We want to develop an infrastructure where
computational experiment e that has been developed
at time t on a hardware and ...
CoESRA
CoESRA
CoESRA Home page
Registration
and login via
AAF
Virtual Desktop on Browser
IUCN Red List Ecosystem Assessment
of Mountain Ash Forest
Mountain Ash Forest Ecosystem Risk Assessment
• Unique biodiversity,
• World tallest flowering plants (over 100 m),
• Cont...
Application of IUCN Red List of Ecosystems Categories and Criteria
No. of Hollow bearing trees
Temp and precipitation
Spat...
Mountain Ash Forest risk assessment workflow
Sub- Workflow for Criteria A
Select Evaluation
Workflow
CoESRA
 Access to cloud-based linux desktop via a
browser
 Virtual desktop comes with Kepler scientific
workflow and oth...
TERN is supported by the Australian Government through
the National Collaborative Research Infrastructure Strategy
and the...
CoESRA: Platform for collaborative research
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CoESRA: Platform for collaborative research

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The presentation provides an overview of CoESRA, a cloud-based platform to build, execute and share complex analysis and synthesis experiments. The infrastructure is offered as "Platform as a Service in virtual desktop. The presentation is part of the Workshop on Approaches to Terrestrial Ecosystem Data Management : from collection to synthesis and beyond

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CoESRA: Platform for collaborative research

  1. 1. Collaborative Environment for Ecosystem System Science Analysis and Synthesis (CoESRA) Presentation by Siddeswara Guru
  2. 2. Outline • Motivation • Reproducible science • Challenges • CoESRA • Use Case: IUCN Red List of Ecosystems Assessment. • Summary
  3. 3. Motivation Reproducible Science Duplicate the scientific experiments or reproduce experiment results. Source: nature.com
  4. 4. Challenges • Lack of culture to make scientific claims reproducible • Lack of detailed information about data and code even after they are published • “lack of an integrated infrastructure for distributing reproducible research to others”1 • Despite the journal Biostatistics’ policy since 2009, as of 2011 only 4% of articles had “R” kite-mark. • In US, $28 billion per year spent on clinical research that are not reproducible2. 1Peng, Roger D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226-1227. doi: 10.1126/science.1213847 2Freedman, L. P., Cockburn, I. M., & Simcoe, T. S. (2015). The Economics of Reproducibility in Preclinical Research. PLoS Biol, 13(6), e1002165. doi:10.1371/journal.pbio.1002165 Source: experimentalmath.info
  5. 5. Reproducibility Spectrum Peng, Roger D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226-1227. doi: 10.1126/science.1213847
  6. 6. Integrated Infrastructure • Cloud-based platform • Scientific workflows executable on a easily accessible platform "one of the most effective ways to promote high-quality science is to create free open-source tools that give scientists easier and cheaper ways to incorporate transparency into their daily workflow:"3 3 Stuart Buck, Solving reproducibility, Science 26 June 2015: 348 (6242), 1403. [DOI:10.1126/science.aac8041]
  7. 7. Scientific workflow • Series of structured interconnected computational activities • Visual front-end to build experiments using components. • Components can be implemented in high-level and/or scripting languages.
  8. 8. Kepler Scientific workflow Features • Ability to create components in different programming languages • Reusable components: actors and Directors • Easy to run workflows as distributed tasks • Platform independent re- usable experiments • Possibility of repeatability and reproducibility
  9. 9. We want to develop an infrastructure where computational experiment e that has been developed at time t on a hardware and software infrastructure h using data d is reproducible at time t1 on same hardware and software infrastructure h using the same data d. Cloud-based virtual desktop accessible to applications and data over a web browser. GOAL
  10. 10. CoESRA
  11. 11. CoESRA
  12. 12. CoESRA Home page Registration and login via AAF
  13. 13. Virtual Desktop on Browser
  14. 14. IUCN Red List Ecosystem Assessment of Mountain Ash Forest
  15. 15. Mountain Ash Forest Ecosystem Risk Assessment • Unique biodiversity, • World tallest flowering plants (over 100 m), • Contribute to water and timber production, • subject to wildfire. • Apply IUCN Red List of Ecosystem criteria for risk assessment2 Source: abc.net.au 2Burns, Emma L., Lindenmayer, David B., Stein, John, Blanchard, Wade, McBurney, Lachlan, Blair, David, & Banks, Sam C. (2015). Ecosystem assessment of mountain ash forest in the Central Highlands of Victoria, south-eastern Australia. Austral Ecology, 40(4), 386-399. doi: 10.1111/aec.12200
  16. 16. Application of IUCN Red List of Ecosystems Categories and Criteria No. of Hollow bearing trees Temp and precipitation Spatial distribution Abundance of hallow bearing trees Degradation through lost bioclimatic suitability Mountain ash forest
  17. 17. Mountain Ash Forest risk assessment workflow
  18. 18. Sub- Workflow for Criteria A
  19. 19. Select Evaluation
  20. 20. Workflow
  21. 21. CoESRA  Access to cloud-based linux desktop via a browser  Virtual desktop comes with Kepler scientific workflow and other tools  Both personal and public storage space  Ability to distribute the execution  Free to use, build and/or execute workflows. Register/login Access to virtual desktop Access CoESRA website
  22. 22. TERN is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy and the Super Science Initiative Project Sponsors collaborators The Workflow shown is accessible from https://www.coesra.org.au Thank you s.guru@uq.edu.au Register/login Access the desktop Access CoESRA website

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